On the bag I am currently working on I wanted a subtle amount of embellishment and decided on a beaded zipper and some beading around the pocket flaps. The zipper is NOT secured by the beads. It is stitched in by machine. The "top" pattern piece consists of two pieces that butt up against the zipper. They are interfaced and then the SA is folded under on one side. The folded side is butted up to the zipper about a 1/16th of an inch away. I then flip it over and stitch in the well of the fold. I really like the clean look of this type of zipper installation. Once the tops are stitched in next to the zipper I marked them. I used a ruler to make a dot every 1/4 inch an equal amount away from the folded edge. This is real important as the beads will want to lay every which way and they do. They are beads. I stitch them on with a back stitch and heavy double thread.
This bag pattern and another Vogue bag that I am working on both have this same type of zipper installation. They both advise whipstitching the upper end of the zipper tape together. This "darts" the zipper in an odd way. If you let the zip lie flat without the whipstitching it lays better but, now you have a space, actually more of a hole. You do get a hole with the whipstitching, just not as big and it bulges a little. This was handled by placing a folded piece of fabric behind the upper edge of the zip and stitching it in when the zipper/top is attached to the gusset.
I like the way it looks now and you can see the results in the top photo.